Chromosome conformation capture (3C) methods identify physical interactions (“contacts") between genomic loci [1]}, [2]}. While classical capture is pairwise, recent advancements capture multi-way chromatin interactions via proximity ligation (Pore-C, Supplement 5.4) [3]}, split-pool tagmentation (SPRITE) [4]}, or multi-contact 3C (MC-3C) [5]}. However, the investigation and biological interpretation of these multi-way contacts is hampered by scarcity of methods for multi-way data [3]}, [7]}.
Hypergraphs are a mathematically tractable extension of graph theory that precisely represent multi-way interactions (Supplement 5.1) [8]}.
We introduce the Hypergraph Analysis Toolbox (HAT), a general purpose software for the analysis of multi-way interactions and higher-order structures. HAT contains both well-studied and novel mathematical methods for hypergraph analysis in both MATLAB and Python.
